Switched! -A Supergirl bodyswap story
by Drawn2write
Summary: Kara and Alex investigate a possible Cadmus weapons Cache, but things take a turn when the sisters switch bodies! Having to keep the switch a secret from all but a few close allies, will Kara and Alex find a cure? And can they manage to live in each others bodies without ruining their lives? Read and find out! Set during season 2 before the events of episode 14
1. Chapter 1

Chapter 1- it begins!

 **Saturday, 6.45 am:**

The electronic shriek of the alarm clock pierced the blackness of the room. For a moment the shriek went unanswered, then gradually movement came. A hand flopped out from within the bundle of covers, searching for the snooze button with hazy determination. Alex Danvers sighed, her eyes half-closed against the flashing display of the clock, now silenced. Alex sat upright in bed and began turning slowly outward, slipping out of bed as quietly as she could. As she gently lowered her feet onto the soft carpet Alex grinned, tiptoeing to the bathroom like a silent shadow. Or so she thought.

Suddenly a groan could be heard coming from the bed as Maggie Sawyer sat upright in the middle of the covers. Alex smiled sheepishly at the disgruntled look on her girlfriend's face. "Sorry, did I wake you? I was trying to be quiet" Alex slipped on a pair of trousers in the near dark as she spoke, continuing to get ready. Maggie just smiled wryly. "Oh, it's fine babe, really! I just love being woken up at the crack of dawn!" she delivered the line in a teasing tone, rubbing sleep from her eyes. "I can't believe you choose to be up this early!...and it's so you can go jogging? You're not Supergirl, you know that, right?" Alex laughed as she slipped on her top, throwing aside the old _Bare Naked Ladies_ t-shirt she had been sleeping in. "You know me, I like to keep healthy!" Alex smiled brightly as she pushed earphones into her ears and limbered up "There's nothing like a casual jog around the city as it wakes up! Plus, this is the only way I can get some exercise in before I meet my sister for breakfast and then head over to the DEO."

Maggie groaned dramatically in response "You have time to do all that? I really am dating a superhero!" She paused to watch the tips of Alex's ears turn pink as she blushed deeply, grinning like a schoolgirl. Maggie smiled at how adorable her girlfriend looked before she turned over, settling back to sleep. "Tell your sister I said hi, ok?"

 **Saturday, 8.00 am:**

It was moments like this that made Kara truly see earth as her home. As she floated in the sky above National City, Kara thought of her lost home of Krypton and felt a twang of grief, her heart aching at the memory of the destruction of her home planet and her journey to earth. For Kara it was a bittersweet memory. She thought she'd lost everything with the fall of Krypton, yet her adopted planet had given her so much. Friends. Family. A purpose far greater than she could have ever imagined. And something else too. Kara thought of Mon-El, how their relationship had changed so much and become so complicated, before it got perfectly simple again. Kara thought of Valentine's day and smiled softly. Mon-El may have some annoying habits, like his refusal to get out of bed before 10 on a Saturday, but he did have _some_ redeeming qualities.

The wind rustled Kara's hair lightly as she scanned the city, watching people carry out their morning routines and she couldn't help but sigh, the scenes of normalcy calming her. Kara felt her phone buzz, signaling a text message. She unlocked her phone and smiled as she scanned the message which read "Hey Kara, got here before you (for once!) I'll order the usual, love Alex -P.S. Maggie says 'hi'" Kara couldn't help but feel her heart swell as she thought of Alex, her adoptive sister and pillar of support for so many years. Krypton and its destruction would always be a part of her, but that didn't mean she was without family.

Kara may be a child of krypton but she was now one of National City's protectors. She was Kara and Supergirl, and as she flew downtown to meet Alex for breakfast, Kara realized she wouldn't have it any other way.

 **Saturday, 9.00 am:**

Alex walked into the control room of the DEO, draining the last of her coffee as she reached the edge of the desk where Winn was typing frantically, his face screwed up in concentration. The screen of Winn's computer flashed with satellite images as a minimized window seemed to be running some sort of algorithm, scanning for an energy source. Alex opened her mouth to ask Winn what this setup was all about as she spotted J'onn entering the room. Alex could practically see the veins bulging in Winn's forehead as his fingers flew across the keys in a frantic blur, and thinking it better to leave him undisturbed she approached J'onn, nodding to him.

"Hey J'onn, what's going on with Winn over there? He looks like he's about to blow a fuse or something!" J'onn shot a quizzical look at Winn as he turned to Alex. "Mr. Schott here thinks he may have found a way to track a cache of weapons which is property of our 'friends' over at Cadmus." Suddenly a whooshing noise interrupted J'onn as Supergirl touched down in the control room, looking less than pleased. "Sorry I'm late, I had to stop a school bus rolling of a bridge- Did you say Cadmus? I may have eavesdropped a little" Kara pointed to her ears as she closed the distance between herself, J'onn and Alex "Super-hearing, remember?" J'onn nodded in confirmation to her first question as Kara groaned, her hand on her forehead. "I feel like everywhere we turn Cadmus is always a step ahead of us! They kidnapped me and Mon-El, put the city in jeopardy and we're just left to pick up the pieces!" Alex reached forward, putting her hand on her sister's shoulder. "Well not this time, ok Kara? I mean Winn looks like he's working overtime and-"

"BOOYAH! Who's your daddy?!". The group turned to see Winn standing over his upturned chair, fist clenched in a mid-air victory pose, almost panting from his efforts. " ?" J'onn said sternly, fixing Winn with a deadpan stare. Winn gulped loudly, clearing his throat before speaking "Yeah, um, sorry about that, I was just totally tracking down the location of a top-secret cache of Cadmus weapons!" Winn beamed with pride as he explained his methods.

"Ok, so I noticed that there have been these weird energy sources kind of popping up out of nowhere all over the city and then disappearing just as quick-" he rubbed his eyes clearly exhausted "-so last night I stayed up all night and kept watch, compiling any instances of the energy signature and eventually I was able to create an algorithm to back-track the energy bursts to an abandoned warehouse near the docks." Alex moved to Winn's screen, looking at the satellite image. "No offence Winn, but I don't see what this has to do with Cadmus. It could be anything really." Winn grinned as he fixed his chair, sitting back down. "I took the liberty of investigating the warehouse itself. It's owned by a discontinued tech company. Nothing weird there right? But then I dug deeper." Winn leaned back in his chair triumphantly. "I was able to uncover a trail of shell companies that eventually lead to one name: Lillian Luthor."

Kara tensed at the mention of the name, her hands balled into fists. "Whatever's going on in that warehouse we have to investigate, right now!" J'onn nodded, motioning to Alex. "Alex, Supergirl is right, time is critical here. That's why I'm sending you two on ahead. You'll act as a recon team without drawing too much attention, but you should still be ready for some resistance." Alex gave a curt nod as Winn prepared the coordinates. "Oh, and one more thing." J'onn said as Supergirl headed for the exit, "Alex I want you wearing a bodycam on this one. There could be critical intel in there and any advantage is welcome." Alex headed toward the armory addressing J'onn over her shoulder as she went "Understood. I just hope we get something that'll give us the edge for once."

 **Saturday, 12.00 pm:**

Supergirl touched down next to Alex's car, joining her sister for the walk to the warehouse. Alex cleared her throat, breaking the silence that hung between them. "You're being quiet, is everything all right? I mean it's important that we keep cool heads on mission and-" Supergirl sighed pushing an unruly strand of hair behind her ear as they closed the distance to the warehouse. "It's Mon-EL. I just keep thinking of what Cadmus put him through, and now that we're sort of together it's like, I feel like as long as they're out there we're not safe…or he's not safe, I guess."

Alex shot her sister a sympathetic look. "Believe it or not I think I know how you feel. I mean my girlfriend is a cop! The threat of violence or injury is always there to some degree. But that's what a relationship is. It's worrying about the person you care about, it's wanting the best for them, always. You know what your worries tell me?" Supergirl looked to Alex shaking her head. "It tells me Mon-El is important to you. That your relationship has the potential to be something truly special! We will stop Cadmus Kara and when we do, you and Mon-El can focus on what you have. Together." Supergirl breathed a sigh of relief, Alex's words calming her. She was turning to thank her when suddenly a crashing sound erupted from inside the warehouse followed swiftly by a blood curdling scream.

Alex strode into the warehouse weapons free, her eyes alert and scanning, ready for hostiles. With a soft click Alex activated the body cam J'onn had instructed her to wear, sending a live feed to the DEO. As Supergirl checked the perimeter Alex made sure to focus the camera on the shelves of Alien tech that lined the walls of the warehouse, most of it defunct, all of it stolen. Supergirl walked through the entrance and put a hand on Alex's shoulder, turning to her. "Alex, I did a sweep of the warehouse with my x-ray vision and I got nothing, no-one's here…well no-one alive anyway." Supergirl motioned for Alex to follow her leading her to a battered door fitted with a rusted lock. With a swift kick Alex broke the door down, stepping inside.

The source of the earlier scream lay in front of them. The singed remains of a man in a lab coat lay on the floor, with smoke still rising from marred flesh. Alex moved to identify the body when suddenly a loud humming filled the room, and the warehouse itself. "Where's that coming from?" Alex roared as the noise began to build, drowning her out. Supergirl scanned the mass of Alien tech littering their surroundings. "I don't know! We have to get out of here, there's-" Suddenly an electric blue flash filled the air, flooding the room.

Supergirl turned to Alex and reading the shock and fear on her face, she grabbed her. Supergirl wrapped her arms around Alex, using her body to shield her from the blast in the seconds before it hit. Supergirl felt the energy about to wash over her, and she knew all she could do was hope to Rao that Alex would be ok.

As Supergirl grit her teeth, preparing for the pain the energy wave reached her, filling her body with an unexpected tingling sensation. The sensation built in intensity then suddenly it was gone as Alex and Supergirl collapsed into the inky blackness of unconsciousness.

 **Saturday, 1.00pm:**

Alex Danvers groaned weakly. Her head felt fuzzy and numb like cotton wool, and the lights of the DEO medical bay stung her eyes. "There's our girl." Winn smiled as Alex pushed herself out of the medical bed wincing slightly as she stood up straight. J'onn flashed a relieved smile at Alex as he entered the room, approaching her. "We were worried for a minute there. You and your sister were exposed to an unknown energy source but as far as we can tell you're both unharmed." Alex breathed a sigh of relief. "Where is my sister? Is she here?" Winn indicated the bed behind the curtain at the end of the medical bay. What Alex saw when she turned moved past the curtain nearly made her pass out again.

Alex was staring down at herself, except there wasn't a mirror there. Lying in the bed behind the curtain was Alex her eyes wide in surprise, her mouth hanging open in disbelief. Alex could do little but return the stare to the imposter before her. Winn approached the sisters clearly puzzled. "Um earth to team Supergirl! Are you guys alright?" He turned to Alex "Kara are you good?" The Alex that was laying on the bed spluttered in indignation. "She's not Kara! I am! What's going on here? And…why is my voice so weird?" Suddenly it hit Alex like a ton of bricks.

The disorientation from the explosion had clouded her judgement but there were subtle tells that seemed glaringly obvious now. The difference in height, the changed gait as she walked over to see her sister, even the fact that Winn was being so chummy with her. Alex ran her hands through her hair, feeling long blonde hair cascade over her face. Winn was making some joke about 'Alex' getting another once over from the paramedics, but Alex cut her off. "She's right." Said Alex simply "She is Kara, and I'm Alex! We…we've switched bodies!"

 **Dun Dun Dun! Thanks so much for reading my first work here! please feel free to check out my profile and add/message me with suggestions. Thanks!**


	2. Chapter 2

**The story so far:** After following a trail of irregular energy pulses throughout the city, Winn zeroed in on an abandoned warehouse, which seemed to house a possible cache of Cadmus tech. Alex and Kara went looking for answers, but the only thing they found was a disfigured corpse and an explosion that had an unexpected impact on the Danvers sisters….

 **Saturday, 1.05pm, DEO medical bay:**

Kara felt as if the med bay was spinning as she stood up from her bed, unable to make sense of what had happened. The last thing she remembered she was shielding Alex from an explosion….but now..she _was_ Alex! Or at least she was in her body somehow. She stumbled over to a stainless steel medical tray on unsteady legs, the reality of the situation refusing to sink in, even as she heard her sister's panic-stricken voice as she ran her hands through her blonde hair. Or is that _my_ blonde hair? Kara thought numbly. Finally she reached the medical tray and slowly picked it up with trembling fingers.

She knew what was going on, as impossible as it seemed, she knew. But still she _had_ to see it. Kara let out a sharp gasp as she caught her reflection in the medical tray. Staring back at her in the reflection was the face or her sister Alex. "no…." Kara whispered in shock as she pulled her cheeks or turned her head, inspecting her face carefully. The reflection followed her movements perfectly. So it was true. Kara felt her knees buckle and suddenly J'onn was beside her, catching her before she could fall. "Alex, are you ok?" his voice was heavy with concern as he supported her body. "I'm….not...not Alex" Kara muttered weakly. J'onn's face was a mixture of confusion and worry. " you and Kara are just confused-" Kara raised her hand cutting him off. "Scan my mind" she said simply. J'onn raised his hand to Kara's temple gently, his eyes turning red as he made use of his Martian powers. Kara watched as the truth hit J'onn, his expression transforming to one of pure shock. "Kara?" the word came out as a gasp "how? I-I don't know how this is possible…." Suddenly Winn's voice could be heard from the other side of the medical bay.

"KARA! Kara calm down!" Alex groaned and covered her ears as Winn tried to reason with her. "I'm NOT Kara damn it!" she called out for what felt like the hundredth time. "We keep going in circles here, but it's me! It's Alex!" Even hearing her words come out in her sister's voice was a bizarre experience, nevermind the fact she was somehow in Kara's body as well. This whole thing was like a horrible nightmare. Being in Kara's body was _not_ fun. Her hair was too long and kept getting in the way, and her outfit was a whole other story. Sure the suit was cool to look at, but wearing it was something else entirely! The boots felt clunky and awkward and the cape kept making irritating rustling noises, not to mention the skirt! Alex couldn't help but feel a little exposed, and if she wasn't so busy being freaked out she'd probably feel a little embarrassed. She looked at Winn in exasperation as he prepared to tell her again that she was wrong. However, before Winn could speak, J'onn came over. "Agent Schott, stand down." He said sternly as he approached, "You are indeed talking to Alex. Somehow their minds have been swapped and they have in effect switched bodies."

For a long time Winn was silent, taking in the new information. Finally he spoke up and turned to Alex. "So I'm confused! Am I the only one or?" Alex cleared her throat. "Ok, look I'm in Kara's body and vice versa. That explosion obviously caused this so all we have to do is find whatever tech caused this and like, reverse-engineer it or whatever." Kara walked over slowly, looking down at her body with each step. "I'm with...Alex" she said in a haze as she looked at her sister, still unable to believe they had really swapped places. Winn took a deep breath and fixed his eyes on the floor. "Yeah, just a slight problem with that guys…..The DEO already processed the scene. All we've got is a bunch of unknown alien tech and a body. We don't even know which bit of tech caused the explosion which did the...switcheroo."

Kara groaned, looking at her feet in dejection, when something caught her eye. Since she was Alex's body now, the bodycam was strapped to 'her' body armour. "Winn! What about this? You can scan the footage we picked up and try and locate the source of this whole mess!" Winn slapped his forehead. "I'm such an idiot! With all this switchy stuff I completely forgot about that! Great catch Alex!" Kara winced as Winn caught himself. " I meant Kara!, great work….Kara...I'm sorry this is just a lot to take in"

Suddenly Alex felt a surge of anger and she grabbed out for Winn, taking a hold of his collar. "You think this is hard for you!? You just have to switch names when you talk to us, we're the ones who switched bodies!" Winn began to babble incoherently as J'onn stepped in scowling. "Agent Danvers you need to calm down right now!" Alex turned to J'onn and was startled by how stern he looked. "J'onn...I" He took another breath, stopping her from finishing the sentence. " I repeat. You _need_ to calm down" he said in a more even but still serious tone. Alex suddenly realised why J'onn had gotten so upset. Without thinking she had grabbed at Winn, not taking into account the fact that she now had super strength. The folds of Winn's collar were held tight in her hand as she held him high up in the air, his feet kicking out in a state of panic.

All at once shame filled Alex and she dropped Winn heavily, hearing a gasp of pain from him as he landed on his hands and knees. Suddenly she was looking at herself kneeling beside Winn, as Kara came to comfort him. "Winn, oh my God I'm so sorry" Alex said, looking down at her hands, only beginning to realise the full implications of being in her sister's body.

After around twenty minutes (and a number of apologies) Winn, Kara and Alex sat in the medical bay. J'onn had left to check on the other agents to make sure their absence wasn't raising too many questions. Kara looked over at Alex and despite the situation couldn't help but smile. Alex might be in her body but one of the upsides (if not the only upside) was Kara was finally able to see how she looked in her super suit, without the annoyance of trying to strategically angle mirrors. Alex caught Kara staring and shot her a confused look. "What's with the goofy look Kara?" there was a twinge of annoyance in Alex's voice as she spoke. Kara sat up clearing her throat. "Well first of all, I'm literally wearing your face so if I look goofy that's on you" Kara said jokingly as she watched the beginnings of a smile pull on the corners of Alex's lips. "And secondly, I was just thinking that it's kind of cool that I can get a proper look at suit.

I honestly didn't realise how well it came out!"

Winn grinned, leaning forward with a prideful smile. "Well of course it's awesome! It was made by the gifted hands of yours truly!" Winn raised his hand to silent ALex as she opened her mouth to speak. "And before you apologise again, I already forgive you!...on one condition" Kara turned to Winn with a look of confusion as Alex nodded "Sure, ok what is it?" Alex replied, still feeling ashamed of herself. Winn smiled and said simply "do a twirl." Alex arched an eyebrow as Kara let out a surprised chuckle. Alex narrowed her eyes "Excuse me?" "Oh come on!" Winn returned "Kara has been wearing that suit for so long but she's never been able to see how it looks on her! Come on now, you wouldn't take this opportunity away from your sister would you?" Alex couldn't suppress a smile as she turned to look at Kara. "What do you think of this?" Kara grinned sheepishly "Well one twirl couldn't hurt, right?"

Ten minutes later J'onn walked in to find Alex laughing and throwing out dramatic twirls as Winn and Kara cheered and called out praise. This came to an abrupt stop when J'onn cleared his throat loudly. "I'm glad you are all in such high spirits" J'onn said evenly taking a deep breath before his next sentence. "I'm afraid I have some bad news. I didn't just leave to check in with the other agents, I also needed some space to think. Objectively" Kara and Alex shared a look of confusion as J'onn continued. "I'm sure I don't have to tell you that your...situation effects more than the workplace. Who you are is tied to your personal lives. If anyone was to find out what happened here it could jeopardise Kara's secret identity and put Alex and her loved ones in danger. That is why I have to tell you both; we need to keep this situation secret from everyone except for the people in this room right now. Do I make myself clear?"

Alex and Kara looked at each other, and suddenly the situation they found themselves went from bad to worse….


End file.
